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- EMDB-36918: Cryo-EM structure of Oryza sativa HKT2;1 at 2.5 angstrom -

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Basic information

Entry
Database: EMDB / ID: EMD-36918
TitleCryo-EM structure of Oryza sativa HKT2;1 at 2.5 angstrom
Map data
Sample
  • Complex: OsHKT2;1 dimer
    • Protein or peptide: Cation transporter HKT2;1
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: Phosphatidylinositol
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: SODIUM IONSodium
  • Ligand: water
KeywordsHKT / K+ transporter / Channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


sodium ion transmembrane transporter activity / symporter activity / potassium ion homeostasis / monoatomic cation transmembrane transporter activity / sodium ion transport / potassium ion transport / plasma membrane
Similarity search - Function
Cation transporter / Cation transport protein
Similarity search - Domain/homology
Cation transporter HKT2;1
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsWang X / Shen X / Qu Y / Wang C / Shen H
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Plants / Year: 2024
Title: Structural insights into ion selectivity and transport mechanisms of Oryza sativa HKT2;1 and HKT2;2/1 transporters.
Authors: Xiaohui Wang / Xiaoshuai Shen / Yannan Qu / Heng Zhang / Chu Wang / Fan Yang / Huaizong Shen /
Abstract: Plant high-affinity K transporters (HKTs) play a pivotal role in maintaining the balance of Na and K ions in plants, thereby influencing plant growth under K-depleted conditions and enhancing ...Plant high-affinity K transporters (HKTs) play a pivotal role in maintaining the balance of Na and K ions in plants, thereby influencing plant growth under K-depleted conditions and enhancing tolerance to salinity stress. Here we report the cryo-electron microscopy structures of Oryza sativa HKT2;1 and HKT2;2/1 at overall resolutions of 2.5 Å and 2.3 Å, respectively. Both transporters adopt a dimeric assembly, with each protomer enclosing an ion permeation pathway. Comparison between the selectivity filters of the two transporters reveals the critical roles of Ser88/Gly88 and Val243/Gly243 in determining ion selectivity. A constriction site along the ion permeation pathway is identified, consisting of Glu114, Asn273, Pro392, Pro393, Arg525, Lys517 and the carboxy-terminal Trp530 from the neighbouring protomer. The linker between domains II and III adopts a stable loop structure oriented towards the constriction site, potentially participating in the gating process. Electrophysiological recordings, yeast complementation assays and molecular dynamics simulations corroborate the functional importance of these structural features. Our findings provide crucial insights into the ion selectivity and transport mechanisms of plant HKTs, offering valuable structural templates for developing new salinity-tolerant cultivars and strategies to increase crop yields.
History
DepositionJul 25, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36918.png

Downloads & links

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Map

FileDownload / File: emd_36918.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.54 Å/pix.
x 480 pix.
= 258.552 Å		0.54 Å/pix.
x 480 pix.
= 258.552 Å		0.54 Å/pix.
x 480 pix.
= 258.552 Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.53865 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0155
Minimum - Maximum-0.048417367 - 0.0787597
Average (Standard dev.)0.000032018455 (±0.001424477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 258.552 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36918_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36918_half_map_2.map
Projections & Slices
AxesZYX

Projections

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : OsHKT2;1 dimer

EntireName: OsHKT2;1 dimer
Components
  • Complex: OsHKT2;1 dimer
    • Protein or peptide: Cation transporter HKT2;1
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: Phosphatidylinositol
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: SODIUM IONSodium
  • Ligand: water

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Supramolecule #1: OsHKT2;1 dimer

SupramoleculeName: OsHKT2;1 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)

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Macromolecule #1: Cation transporter HKT2;1

MacromoleculeName: Cation transporter HKT2;1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)
Molecular weightTheoretical: 60.822293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK GGRMTSIYHD FIHNKLQSFG RIGRYFVNFV VLAHRFIALH IHPFWIQLSY FLLISILGSV LLMFLKPSNP EFRPGYIDM LFLSTSALTL SSLITIEMEV LSSSQIVVIT LLMLLGGEVF VSFLGLMLRL NHKHNPEFSG DKVSSVPIEL D TINSASTV ...String:
MADYKDDDDK GGRMTSIYHD FIHNKLQSFG RIGRYFVNFV VLAHRFIALH IHPFWIQLSY FLLISILGSV LLMFLKPSNP EFRPGYIDM LFLSTSALTL SSLITIEMEV LSSSQIVVIT LLMLLGGEVF VSFLGLMLRL NHKHNPEFSG DKVSSVPIEL D TINSASTV ISCEELQLEA AIPEVPSSTI KDLKRSKRLR WFLGFVVFSY FVVIHVAGFL LVLWYISRVS SAKAPLKKKG IN IALFSFS VTVSSFANVG LVPTNENMAI FSKNPGLLLL FIGQILAGNT LYPLFLRLLI WFLGKVTKLR ELKLMIKNPE ELQ YDYLLP KLPTAFLAST VIGLMASLVT LFGAVDWNSS VFDGLSSYQK IINALFMAVN ARHSGENSID CSLIAPAVLV LFII LMYLP PSTTFALSNG DEKTANKKAK RKLGLVVQNL AFSQLACISV FVIVAFITER SRLRNDPLNF SALNMIFEII SAYGN VGLS TGYSCSRLQK LHPGSICQDK PYSLSGWWSD EGKLLLVFVM LYGRLKAFTK GTGEYWRLW

UniProtKB: Cation transporter HKT2;1

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: Phosphatidylinositol

MacromoleculeName: Phosphatidylinositol / type: ligand / ID: 3 / Number of copies: 2 / Formula: T7X
Molecular weightTheoretical: 887.128 Da
Chemical component information

ChemComp-T7X:
Phosphatidylinositol / Phosphatidylinositol

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Macromolecule #4: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 4 / Number of copies: 2 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

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Macromolecule #5: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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Macromolecule #6: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 2 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM / Phosphatidylcholine

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Macromolecule #7: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 7 / Number of copies: 4
Molecular weightTheoretical: 22.99 Da

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 130 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 501277

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